But when Pedroia fouled the ball high behind the plate, Nava’s instincts kicked in.

“I just stopped thinking,” the 30-year-old outfielder said.

Nava tagged up and darted toward second. He was thrown out by Yankees catcher Chris Stewart for an inning-ending double play.

“I wasn’t on top of what I should’ve been on top of,” Nava said. “It’s those little things.”

Base-running blunders plagued Boston in a 5-2 loss to the Yankees on Saturday at Fenway Park. In a game where they only mustered seven hits, the Sox were tagged out twice at home plate.

That’s not to mention the seventh inning when Ortiz disobeyed orders from third base coach Brian Butterfield. As Butterfield signaled to stay when Jonny Gomes flied out to deep center field, Ortiz — all 6 feet 4 inches and 250 pounds of him — ran home.

The designated hitter scored, easily.

Manager John Farrell and his staff have preached aggressiveness on the bases since spring training.

The new approach has been mostly successful. The Sox entered Saturday atop the American League in stolen bases and success rate on steals.

“We run the bases well,” first baseman Mike Carp said. “We’ve done a good job all year moving guys, shuffling first to third, things like that.”

The rewards are great — Boston also entered Saturday leading the AL in runs scored — but the risks are high.

When the Sox don’t execute, it can be costly — and it seems to come in bunches. Two runners were also tagged out at home in a 6-2 loss to the Blue Jays in June.

“It’s a fine line,” Farrell said. “Game situation is going to dictate most of it, if not all of it. It worked against us a couple of times today.”

Nava also faltered in the first inning when standing on second with two outs. Ortiz smacked a two-out single to left field. Butterfield said go. Nava ran fast, but as he rounded third, he stumbled.

The throw home beat Nava by several steps. What if he hadn’t stumbled?

With two outs in the fifth, Boston had two runners in scoring position. A pitch from Yankees starter Hiroki Kuroda bounced in the dirt and went past Stewart. Carp tried to score from third. He, too, was tagged out.

“At that point in the game, you want to score a run and get things rolling for the team,” said Carp, who defended the decision to run with the Yankees leading, 1-0.

Carp said he knew Kuroda’s split-fingered pitches sometimes end up in the dirt. All game Carp knew if a pitch got away, he had a shot.

“We all thought we had really good breaks,” Carp said. “I thought myself that I had a good break.”

Nava’s eighth-inning mistake was perhaps the most costly because of the timing. The Sox had rallied to halve a 4-0 deficit in the seventh inning, finally cracking into the Yankees’ bullpen.

It was a fluky play. Stewart dived into the stands to snag the ball. His throw to second was pristine.

“That was over-aggressiveness on [Nava’s] part,” Farrell said.

“That’s a time where, even if you can take the base, I shouldn’t have taken the base,” Nava said. “Looking back, I wouldn’t have done it.”

But the Sox can’t change the past — and they won’t change their approach.

“It comes down to being aggressive,” Carp said. “You want to be aggressive making mistakes. That’s the best way to do it.”

Carp pointed to the success the Sox have had with base running all year. One game does not erase that, he said.